/*
Copyright (c) 2012, Geoffrey Ong
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
    * Redistributions in binary form must reproduce the above copyright
      notice, this list of conditions and the following disclaimer in the
      documentation and/or other materials provided with the distribution.
    * Neither the name of the <organization> nor the
      names of its contributors may be used to endorse or promote products
      derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "boolean.h"

#ifndef SETTING_STRUCT
#define SETTING_STRUCT
typedef struct Setting
{
  char* outputFile;
  char* dataDir;
  int numProcessors;
  boolean preprocess;
  float kappa_Start;
  float kappa_Increment;
  float kappa_Finish;
  float dp_Gap_Open_Start;
  float dp_Gap_Open_Increment;
  float dp_Gap_Open_Finish;
  float dp_Gap_Continue_Start;
  float dp_Gap_Continue_Increment;
  float dp_Gap_Continue_Finish;

}Setting;
#endif

#ifndef ATOM_STRUCT
#define ATOM_STRUCT
typedef struct Atom
{ 
  int index;
  float coorx;
  float coory;
  float coorz;
  float lambda;
  float bFactor;
  float ssd;
  char acid[3];
}Atom;
#endif

#ifndef PROTEIN_STRUCT
#define PROTEIN_STRUCT
typedef struct Protein
{
  int index;
  char* name;
  int size;
  Atom* atom;
}Protein;
#endif

#ifndef LAMBDA_SCORE_STRUCT
#define LAMBDA_SCORE_STRUCT
typedef struct Lambda_Score
{
  float* row;
  float* column;
  // Perhaps a modified 2-D Array
  // A to B
  // A_Length x B_Length
}Lambda_Score;
#endif

#ifndef DP_SCORE_STRUCT
#define DP_SCORE_STRUCT
typedef struct DP_Score
{
  float* row;
  float* column;
  // Total Size: All Proteins
}DP_Score;
#endif

#ifndef SETTING_FUNCTIONS
#define SETTING_FUNCTIONS
Setting *readSettings();
void printSettings();
void deleteSettings(Setting settings);
#endif

#ifndef PROTEIN_FUNCTIONS
#define PROTEIN_FUNCTIONS
Protein *readProtein(char* dataDir, char* proteinFile, int index);
void writeProtein();
void printProtein(Protein *protein);
void printAtom(Atom *atom);
void deleteProtein(Protein *protein);
void deleteAtom(Atom *atom);
#endif
